Recep Tayyip Erdogan accused the head of the Kurdistan Regional Government of "treachery" for pressing ahead with the vote despite international opposition.
Massoud Barzani should now "give up on this adventure", he said.
Mr Erdogan has previously threatened to cut a vital Kurdish oil pipeline and stop lorries crossing Turkey's border.
Turkey fears that the emergence of an independent Kurdish state on its border will stoke separatist feeling in its own Kurdish minority.
Iraqi Prime Minister Haider al-Abadi ruled out any such talks on Monday night, saying he would not discuss the referendum's results because it was "unconstitutional".
'Sabre-rattling for domestic audience'
This was the strongest rhetoric yet from President Erdogan on the Kurdish referendum. He called it "treachery" and a "threat to national security". Once again he threatened military or economic intervention, without elaborating.
Turkey is worried that independence might further Kurdish insurgency here and is concerned for ethnic Turkmen in the city of Kirkuk, which the Kurds want to be part of any future state. But there was a lot for a domestic audience - sabre-rattling to please nationalists at home.
Ankara has built a strong relationship with the Iraqi Kurds through an oil pipeline that feeds the Kurdish economy and Turkey's energy needs. And the authorities in Irbil oppose the PKK Kurdish militant group, allowing Turkish military bases in northern Iraq. Mr Erdogan warned he could close the oil valves in Turkey - but it has not yet happened.
With Turkey's notoriously abrasive president, the oratory sometimes does not actually translate into action.
Iraqi Kurdish referendum: What is at stake?
Iraqi Kurdistan profile
In a speech on Tuesday, Mr Erdogan said he had expected "until the last moment" that Kurdistan Regional President Massoud Barzani would postpone the vote.
"This referendum decision, which has been taken without any consultation, is treachery," he said.
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